Imported from samtools-r902
This script was put in a wrong place...
fixed compiling errors
this is for a very special application...
targetcut can be compiled, though probably buggy
fixed an out-of-boundary bug in rare cases
skip unmapped and ref-skip reads in indel calling
Merge branch 'master' into devel
fixed a bug; better scoring
updated .gitignore
point out there are 4 or fewer free parameters
fixed a bug about bit ordering
avoid a segfault when network connect fails
update INSTALL
fixed a bug in tview on big-endian by Nathan Weeks
Merge branch 'master' into devel
SAM output
routine for phasing fosmid resequencing (incomplete)
added testing code
reduce the effect of seq errors at the cost of SN